#!/usr/bin/env python3 # (C) 2026 Cadence Design Systems, Inc. (Cadence) # All rights reserved. # TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is # provided to current licensees or subscribers of Cadence products or # SaaS offerings (each a "Customer"). # Customer is hereby permitted to use, copy, and modify the Sample Code, # subject to these terms. Cadence claims no rights to Customer's # modifications. Modification of Sample Code is at Customer's sole and # exclusive risk. Sample Code may require Customer to have a then # current license or subscription to the applicable Cadence offering. # THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT # NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A # PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be # liable for any damages or liability in connection with the Sample Code # or its use. """Depict a molecule with interactive property pie chart and color gradients.""" import argparse import io import math import os import pathlib import sys from openeye import oechem, oedepict, oegrapheme, oemolprop from PIL import Image from rich_argparse import HelpPreviewAction, RichHelpFormatter __SCRIPT_NAME__ = pathlib.Path(__file__).absolute().stem __SCRIPT_DESC__ = ( "Depict a molecule with interactive property pie chart and color gradients." ) __SCRIPT_TOOLKITS__ = ["oechem", "oedepict", "oegrapheme", "oemolprop"] __SCRIPT_CATEGORIES__ = ["depiction"] def parse_args() -> argparse.Namespace: """Parse command-line arguments.""" parser = argparse.ArgumentParser( add_help=True, formatter_class=RichHelpFormatter, description="[yellow]" + __SCRIPT_DESC__ + "[/yellow]", ) input_group = parser.add_argument_group("Input options") input_group.add_argument( "--mol", type=str, required=True, metavar="MOL-FILE", help="input molecule file", ) image_group = parser.add_argument_group("Image options") image_group.add_argument( "--image", type=str, required=False, metavar="IMAGE-FILE", help="output image file (SVG)", ) image_group.add_argument( "--width", type=int, default=800, help="width of output image (default: %(default)s)", ) image_group.add_argument( "--height", type=int, default=600, help="height of output image (default: %(default)s)", ) display_group = parser.add_argument_group("Display options") display_group.add_argument( "--color-gradient", action="store_true", help="display property value on color gradient (default: %(default)s)", ) parser.add_argument("--help-image", action=HelpPreviewAction) return parser.parse_args() def main() -> int: """Depict a molecule with interactive property pie chart and color gradients.""" args = parse_args() _check_image_file(args) input_stream = oechem.oemolistream() if not input_stream.open(args.mol): oechem.OEThrow.Fatal("Cannot open input file!") mol = oechem.OEGraphMol() if not oechem.OEReadMolecule(input_stream, mol): oechem.OEThrow.Fatal("Cannot read input file!") width, height = args.width, args.height opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) opts.SetMargin(oedepict.OEMargin_Right, 25.0) opts.SetMargin(oedepict.OEMargin_Bottom, 20.0) opts.SetBondWidthScaling(True) clear_coords, suppress_h = True, True prep_opts = oedepict.OEPrepareDepictionOptions(clear_coords, suppress_h) prep_opts.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal) oedepict.OEPrepareDepiction(mol, prep_opts) prop_displays = _get_property_displays() set_properties(mol, prop_displays) image = oedepict.OEImage(width, height) render_properties(image, mol, opts, prop_displays, args.color_gradient) oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0) if args.image: if args.image.lower().endswith(".svg"): icon_scale = 0.5 oedepict.OEAddInteractiveIcon( image, oedepict.OEIconLocation_TopRight, icon_scale ) oedepict.OEWriteImage(args.image, image) else: _img = Image.open(io.BytesIO(oedepict.OEWriteImageToBytes("png", image))) _img.show() return os.EX_OK class OEPropertyDisplay: """Container for a single molecule property display configuration.""" def __init__( self, prop_id: str, label: str, filter_name: bytes, color_gradient: oechem.OELinearColorGradient, value_dict: dict[str, int] | None = None, ) -> None: """Initialize a property display configuration.""" self._id = prop_id self._label = label self._filter_name = filter_name self._color_gradient = oechem.OELinearColorGradient(color_gradient) self._orig_value: str | None = None self._value: float | None = None self._value_dict = value_dict def __str__(self) -> str: """Return a string representation of the property display.""" return f"{self._label} = {self._value}" def get_id(self) -> str: """Return the property identifier.""" return self._id def get_label(self) -> str: """Return the display label.""" return self._label def get_filter_name(self) -> bytes: """Return the OEFilter field name.""" return self._filter_name def set_value(self, value: str) -> None: """Set the property value from a filter output string.""" self._orig_value = value if self._value_dict is not None: self._value = float(self._value_dict[value]) else: self._value = float(value) def get_orig_value(self) -> str | None: """Return the original string value.""" return self._orig_value def get_value(self) -> float | None: """Return the numeric property value.""" return self._value def get_color_gradient(self) -> oechem.OELinearColorGradient: """Return the color gradient for this property.""" return self._color_gradient def get_color(self) -> oechem.OEColor: """Return the color corresponding to the current value.""" if self.get_value() is None: return oechem.OEWhite return self._color_gradient.GetColorAt(self.get_value()) def get_pie_pen(self) -> oedepict.OEPen: """Return a filled pen for drawing the pie slice.""" color = self.get_color() return oedepict.OEPen(color, color, oedepict.OEFill_On, 1.0) def get_label_border_pen(self) -> oedepict.OEPen: """Return a pen for drawing the label border.""" color = self.get_color() return oedepict.OEPen(oechem.OEWhite, color, oedepict.OEFill_On, 3.0) def render_properties( image: oedepict.OEImageBase, mol: oechem.OEMolBase, opts: oedepict.OE2DMolDisplayOptions, properties: list[OEPropertyDisplay], color_gradient: bool, ) -> None: """ Render molecule with an interactive property pie chart overlay. Draws the molecule into the image, then overlays an interactive pie chart showing molecular properties. Hovering over a pie slice displays the property value either as a color gradient or as a text label. """ disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule(image, disp) image_w, image_h = image.GetWidth(), image.GetHeight() pie_frame_size = opts.GetMargin(oedepict.OEMargin_Right) * image_w / 100.0 pie_frame = oedepict.OEImageFrame( image, pie_frame_size, pie_frame_size, oedepict.OE2DPoint( image_w - pie_frame_size * 1.1, image_h - pie_frame_size * 1.1 ), ) color_frame_w = image_w - pie_frame.GetWidth() * 1.25 color_frame_h = opts.GetMargin(oedepict.OEMargin_Bottom) * 0.75 * image_h / 100.0 color_frame = oedepict.OEImageFrame( image, color_frame_w, color_frame_h, oedepict.OE2DPoint(10.0, image_h - color_frame_h - 10.0), ) center = oedepict.OEGetCenter(pie_frame) radius = pie_frame_size / 2.0 inc_angle = 360.0 / len(properties) bgn_angle = 0.0 group_prefix = "property_hover_" for prop in properties: area_group = image.NewSVGGroup(prop.get_id()) hover_group = image.NewSVGGroup(group_prefix + prop.get_id()) oedepict.OEAddSVGHover(area_group, hover_group) image.PushGroup(area_group) _draw_property_pie( pie_frame, prop, center, bgn_angle, bgn_angle + inc_angle, radius ) image.PopGroup(area_group) image.PushGroup(hover_group) label_text = f"{prop.get_label()} = {prop.get_orig_value()}" if color_gradient: _draw_property_color_gradient(color_frame, prop, label_text) else: _draw_property_label(image, prop, label_text) image.PopGroup(hover_group) bgn_angle += inc_angle def _draw_property_color_gradient( image: oedepict.OEImageBase, prop: OEPropertyDisplay, label_text: str, ) -> None: """Draw the property value on a color gradient bar.""" opts = oegrapheme.OEColorGradientDisplayOptions() opts.SetColorStopPrecision(1) opts.SetColorStopLabelFontScale(0.5) opts.AddLabel(oegrapheme.OEColorGradientLabel(prop.get_value(), label_text)) oegrapheme.OEDrawColorGradient(image, prop.get_color_gradient(), opts) def _draw_property_label( image: oedepict.OEImageBase, prop: OEPropertyDisplay, label_text: str, ) -> None: """Draw the property value as a text label.""" font = oedepict.OEFont( oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 18, oedepict.OEAlignment_Center, oechem.OEBlack, ) label = oedepict.OEHighlightLabel(label_text, font) label.SetFont(font) label.SetBoundingBoxPen(prop.get_label_border_pen()) label_pos = oedepict.OE2DPoint(image.GetWidth() / 2.0, image.GetHeight() - 25.0) oedepict.OEAddLabel(image, label_pos, label) def _draw_property_pie( image: oedepict.OEImageBase, prop: OEPropertyDisplay, center: oedepict.OE2DPoint, bgn_angle: float, end_angle: float, radius: float, ) -> None: """Draw a single pie slice for a property.""" pos = _get_pie_label_position(center, bgn_angle, end_angle, radius / 10.0) shadow_offset = oedepict.OE2DPoint(3.0, 3.0) image.DrawPie( pos + shadow_offset, bgn_angle, end_angle, radius, oedepict.OELightGreyBoxPen ) image.DrawPie(pos, bgn_angle, end_angle, radius, prop.get_pie_pen()) label_text = prop.get_id() font_size = int(radius / 5) font = oedepict.OEFont( oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, font_size, oedepict.OEAlignment_Center, oechem.OEBlack, ) label = oedepict.OEHighlightLabel(label_text, font) label.SetBoundingBoxPen(oedepict.OETransparentPen) text_center = _get_pie_label_position(center, bgn_angle, end_angle, radius) oedepict.OEAddLabel(image, text_center, label) def _get_pie_label_position( center: oedepict.OE2DPoint, bgn_angle: float, end_angle: float, radius: float, ) -> oedepict.OE2DPoint: """Compute the label position for a pie slice.""" p = oedepict.OE2DPoint(0.0, -radius / 1.5) mid_angle = (bgn_angle + end_angle) / 2.0 rad = math.radians(mid_angle) cos_rad = math.cos(rad) sin_rad = math.sin(rad) return center + oedepict.OE2DPoint( cos_rad * p.GetX() - sin_rad * p.GetY(), sin_rad * p.GetX() + cos_rad * p.GetY(), ) def set_properties(mol: oechem.OEMolBase, properties: list[OEPropertyDisplay]) -> None: """Compute molecular properties using OEFilter and assign values.""" ifs = oechem.oeisstream(_get_filter_rules()) mol_filter = oemolprop.OEFilter(ifs) level = oechem.OEThrow.GetLevel() oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Warning) output_str = oechem.oeosstream() pwnd = False mol_filter.SetTable(output_str, pwnd) headers = output_str.str().split(b"\t") output_str.clear() mol_filter(mol) fields = output_str.str().decode("UTF-8").split("\t") output_str.clear() filter_dict = dict(zip(headers, fields, strict=False)) for prop in properties: if prop.get_filter_name() in filter_dict: prop.set_value(filter_dict[prop.get_filter_name()]) oechem.OEThrow.SetLevel(level) def _get_filter_rules() -> str: """Return the OEFilter rules string for property computation.""" return """ # This file defines the rules for filtering multi-structure files based on # properties and substructure patterns. MIN_MOLWT 130 "Minimum molecular weight" MAX_MOLWT 781 "Maximum molecular weight" MIN_XLOGP -3.0 "Minimum XLogP" MAX_XLOGP 6.85 "Maximum XLogP" PSA_USE_SandP false "Count S and P as polar atoms" MIN_2D_PSA 0.0 "Minimum 2-Dimensional (SMILES) Polar Surface Area" MAX_2D_PSA 205.0 "Maximum 2-Dimensional (SMILES) Polar Surface Area" # choices are insoluble list[OEPropertyDisplay]: """Build the list of property display configurations.""" sol_dict = { "insoluble": 1, "poorly": 2, "moderately": 3, "soluble": 4, "very": 5, "highly": 6, } return [ OEPropertyDisplay( "MW", "Molecular weight", b"molecular weight", _get_mol_weight_color_gradient(), ), OEPropertyDisplay("XLogP", "XLogP", b"XLogP", _get_xlogp_color_gradient()), OEPropertyDisplay( "TPSA", "Topological PSA", b"2d PSA", _get_tpsa_color_gradient() ), OEPropertyDisplay( "Sol", "Solubility", b"Solubility", _get_solubility_color_gradient(), sol_dict, ), OEPropertyDisplay( "Rof5", "Rule of five", b"Lipinski violations", _get_lipinski_color_gradient(), ), ] def _get_mol_weight_color_gradient() -> oechem.OELinearColorGradient: """Return color gradient for molecular weight.""" mol_weight_mean = 314.0 mol_weight_sigma = 128 color_gradient = oechem.OELinearColorGradient() color_gradient.AddStop(oechem.OEColorStop(0.0, oechem.OERed)) color_gradient.AddStop(oechem.OEColorStop(mol_weight_mean / 2.0, oechem.OEYellow)) color_gradient.AddStop(oechem.OEColorStop(mol_weight_mean, oechem.OEGreen)) color_gradient.AddStop( oechem.OEColorStop(mol_weight_mean + 1.5 * mol_weight_sigma, oechem.OEYellow) ) color_gradient.AddStop( oechem.OEColorStop(mol_weight_mean + 3 * mol_weight_sigma, oechem.OERed) ) return color_gradient def _get_xlogp_color_gradient() -> oechem.OELinearColorGradient: """Return color gradient for XLogP.""" log_p_mean = 2.472 log_p_sigma = 2.013 color_gradient = oechem.OELinearColorGradient() color_gradient.AddStop( oechem.OEColorStop(log_p_mean - 3 * log_p_sigma, oechem.OERed) ) color_gradient.AddStop( oechem.OEColorStop(log_p_mean - 1.5 * log_p_sigma, oechem.OEYellow) ) color_gradient.AddStop(oechem.OEColorStop(log_p_mean, oechem.OEGreen)) color_gradient.AddStop( oechem.OEColorStop(log_p_mean + 1.5 * log_p_sigma, oechem.OEYellow) ) color_gradient.AddStop( oechem.OEColorStop(log_p_mean + 3 * log_p_sigma, oechem.OERed) ) return color_gradient def _get_tpsa_color_gradient() -> oechem.OELinearColorGradient: """Return color gradient for topological PSA.""" t_psa_mean = 62.8 t_psa_sigma = 50.5 color_gradient = oechem.OELinearColorGradient() color_gradient.AddStop(oechem.OEColorStop(0.0, oechem.OERed)) color_gradient.AddStop(oechem.OEColorStop(t_psa_mean / 2.0, oechem.OEYellow)) color_gradient.AddStop(oechem.OEColorStop(t_psa_mean, oechem.OEGreen)) color_gradient.AddStop( oechem.OEColorStop(t_psa_mean + 1.5 * t_psa_sigma, oechem.OEYellow) ) color_gradient.AddStop( oechem.OEColorStop(t_psa_mean + 3 * t_psa_sigma, oechem.OERed) ) return color_gradient def _get_solubility_color_gradient() -> oechem.OELinearColorGradient: """Return color gradient for solubility.""" color_gradient = oechem.OELinearColorGradient() color_gradient.AddStop(oechem.OEColorStop(1.0, oechem.OERed)) color_gradient.AddStop(oechem.OEColorStop(3.5, oechem.OEYellow)) color_gradient.AddStop(oechem.OEColorStop(6.0, oechem.OEGreen)) return color_gradient def _get_lipinski_color_gradient() -> oechem.OELinearColorGradient: """Return color gradient for Lipinski violations.""" color_gradient = oechem.OELinearColorGradient() color_gradient.AddStop(oechem.OEColorStop(0.0, oechem.OEGreen)) color_gradient.AddStop(oechem.OEColorStop(2.0, oechem.OEYellow)) color_gradient.AddStop(oechem.OEColorStop(3.0, oechem.OERed)) return color_gradient def _check_image_file(args: argparse.Namespace) -> None: # script will terminate if there is some issues if not args.image: # image will be displayed on the screen return ext = pathlib.Path(args.image).suffix[1:].upper() if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image output type!") ofs = oechem.oeofstream() if not ofs.open(args.image): oechem.OEThrow.Fatal("Cannot open output image file!") setattr(main, "__SCRIPT_NAME__", __SCRIPT_NAME__) setattr(main, "__SCRIPT_DESC__", __SCRIPT_DESC__) setattr(main, "__SCRIPT_TOOLKITS__", __SCRIPT_TOOLKITS__) setattr(main, "__SCRIPT_CATEGORIES__", __SCRIPT_CATEGORIES__) if __name__ == "__main__": sys.exit(main())